tbuckley/cabot-search huggingface dataset:
CNSC-01. GABAERGIC NEURON-TO-GLIOMA SYNAPSES IN DIFFUSE MIDLINE GLIOMAS
Authors: Tara Barron, Belgin Yalçın, Aaron Mochizuki, Evan Cantor, Kiarash Shamardani, Dana Tlais, Andrea Franson, Samantha Lyons, Vilina Mehta, Samin Maleki Jahan, Kathryn Taylor, Michael Keough, Haojun Xu, Minhui Su, Michael Quezada, Pamelyn Woo, Paul Fisher, Cynthia Campen, Sonia Partap, Carl Koschmann, Michelle Monje
Journal: Neuro-Oncology (2023)

Abstract High-grade gliomas include clinically and molecularly distinct subtypes that stratify by anatomical location into diffuse midline gliomas (DMG) such as diffuse intrinsic pontine glioma (DIPG) and hemispheric high-grade gliomas. Neuronal activity drives high-grade glioma progression both through paracrine signaling and direct neuron-to-glioma synapses. Glutamatergic, AMPA receptor-dependent synapses between neurons and malignant glioma cells have been demonstrated in both pediatric and adult high-grade gliomas, but neuron-to-glioma synapses mediated by other neurotransmitters remain largely unexplored. Using whole-cell patch clamp electrophysiology, in vivo optogenetics and patient-derived glioma xenograft models, we have now identified functional, tumor-promoting GABAergic neuron-to-glioma synapses mediated by GABAA receptors in DMGs. GABAergic input has a depolarizing effect on DMG cells due to NKCC1 expression and consequently elevated intracellular chloride concentration in DMG tumor cells. As membrane depolarization increases glioma proliferation, we find that the activity of GABAergic interneurons promotes DMG proliferation in vivo. Increasing GABA signaling with the benzodiazepine lorazepam – a positive allosteric modulator of GABAA receptors commonly administered to children with DMG for nausea or anxiety - increases GABAA receptor conductance and increases glioma proliferation in orthotopic xenograft models of DMG. Conversely, levetiracetam, an anti-epileptic drug that attenuates GABAergic neuron-to-glioma synaptic currents, reduces glioma proliferation in patient-derived DMG xenografts and extends survival of mice bearing DMG xenografts. Concordant with gene expression patterns of GABAA receptor subunit genes across subtypes of glioma, depolarizing GABAergic currents were not found in hemispheric high-grade gliomas. Accordingly, neither lorazepam nor levetiracetam influenced the growth rate of hemispheric high-grade glioma patient-derived xenograft models. Retrospective real-world clinical data are consistent with these conclusions and should be replicated in future prospective clinical studies. Taken together, these findings uncover GABAergic synaptic communication between GABAergic interneurons and DMG cells, underscoring a tumor subtype-specific mechanism of brain cancer neurophysiology with important potential implications for commonly used drugs in this disease context.
Cardiac Substructure Radiation Dose and Risk of Late Cardiac Disease in Survivors of Childhood Cancer: A Report From the Childhood Cancer Survivor Study
Authors: James E. Bates, Suman Shrestha, Qi Liu, Susan A. Smith, Daniel A. Mulrooney, Wendy Leisenring, Todd Gibson, Leslie L. Robison, Eric J. Chow, Kevin C. Oeffinger, Gregory T. Armstrong, Louis S. Constine, Bradford S. Hoppe, Choonsik Lee, Yutaka Yasui, Rebecca M. Howell
Journal: Journal of Clinical Oncology (2023)

PURPOSE Radiation-associated cardiac disease is a major cause of morbidity/mortality among childhood cancer survivors. Radiation dose-response relationships for cardiac substructures and cardiac diseases remain unestablished. METHODS Using the 25,481 5-year survivors of childhood cancer treated from 1970 to 1999 in the Childhood Cancer Survivor Study, we evaluated coronary artery disease (CAD), heart failure (HF), valvular disease (VD), and arrhythmia. We reconstructed radiation doses for each survivor to the coronary arteries, chambers, valves, and whole heart. Excess relative rate (ERR) models and piecewise exponential models evaluated dose-response relationships. RESULTS The cumulative incidence 35 years from diagnosis was 3.9% (95% CI, 3.4 to 4.3) for CAD, 3.8% (95% CI, 3.4 to 4.2) for HF, 1.2% (95% CI, 1.0 to 1.5) for VD, and 1.4% (95% CI, 1.1 to 1.6) for arrhythmia. A total of 12,288 survivors (48.2%) were exposed to radiotherapy. Quadratic ERR models improved fit compared with linear ERR models for the dose-response relationship between mean whole heart and CAD, HF, and arrhythmia, suggesting a potential threshold dose; however, such departure from linearity was not observed for most cardiac substructure end point dose-response relationships. Mean doses of 5-9.9 Gy to the whole heart did not increase the risk of any cardiac diseases. Mean doses of 5-9.9 Gy to the right coronary artery (rate ratio [RR], 2.6 [95% CI, 1.6 to 4.1]) and left ventricle (RR, 2.2 [95% CI, 1.3 to 3.7]) increased risk of CAD, and to the tricuspid valve (RR, 5.5 [95% CI, 2.0 to 15.1]) and right ventricle (RR, 8.4 [95% CI, 3.7 to 19.0]) increased risk of VD. CONCLUSION Among children with cancer, there may be no threshold dose below which radiation to the cardiac substructures does not increase the risk of cardiac diseases. This emphasizes their importance in modern treatment planning.
MDB-06. PLASMA MEMBRANE PROFILING REVEALS A TARGETABLE CELL-SURFACE PHENOTYPE OF WNT-MEDULLOBLASTOMA
Authors: Jessica T Taylor, James C Williams, Katherine E Masih, Sigourney Bonner, Paul Lehner, Richard J Gilbertson
Journal: Neuro-Oncology (2023)

Abstract WNT-medulloblastoma has an excellent prognosis, with an overall survival rate of 90% among children receiving standard-of-care surgical resection, radiotherapy, and chemotherapy. While curative, this treatment is associated with major, long-term, debilitating side effects. Therefore, it is crucial we develop effective, less toxic therapies for these children. The Gilbertson lab has previously shown that WNT-medulloblastomas are devoid of a Blood-Brain-Barrier (BBB). This disruption allows large molecules such as monoclonal antibodies (mAbs) to penetrate WNT-medulloblastomas. To discover WNT-medulloblastoma specific antigens for mAb targeting, we have first generated bulk and single-cell RNA sequencing profiles of the wild-type and WNT-medulloblastoma-prone mossy-fibre progenitor lineages in the lower rhombic lip, as well as human medulloblastoma patient derived orthotopic xenograft (PDOX) tumours. We next generated plasma membrane proteome profiles of hindbrain germinal zones and WNT-medulloblastomas. Plasma Membrane Profiling (PMP) deploys an isobaric chemical labelling approach -Tandem Mass Tags (TMT) - that allows multiplexing of up to sixteen variables per mass spectrometry experiment and ex vivo TMT-labelling of primary cells. Using this approach, we have mapped the cell surface proteome of our medulloblastoma models. Interrogation of these developmental and tumour data has unmasked WNT-medulloblastoma associated antigens that are specific for prenatal brain and WNT-medulloblastoma, but that are not expressed on critical postnatal tissues. Our workflow integrates multi-omic data sets to uncover a targetable landscape on the surface of WNT-medulloblastoma cells that we have cross-validated with a large cohort of patient RNA sequencing profiles and histological samples of both mouse and human tumours. To translate this dataset to real patient benefit, we are generating high affinity antibodies of these validated cell-surface proteins for assessment in our pre-clinical mouse models. mAbs directed towards essential receptors may have a therapeutic effect alone, however we will additionally modify mAbs to specifically deliver cytotoxic therapeutics - curing children whilst sparing healthy brain tissue.
EPEN-01. ZFTA-RELA FUSION PROGRAMS CONVERGE ON YAP PATHWAY ACTIVATION IN EPENDYMOMA
Authors: Austin Stuckert, Srinidhi Varadharajan, Stephen Mack
Journal: Neuro-Oncology (2023)

Abstract Approximately two thirds of supratentorial ependymoma are driven by the ZFTA-RELA gene fusion. ZFTA is a recently described gene with a role in DNA binding and transcriptional regulation, while RELA (p65) is a known principal mediator of the canonical NFkB pathway, a pathway activated many human malignancies. The underlying mechanism of NFkB pathway protein interaction with the ZFTA-RELA fusion to drive tumorgenesis has not yet been described. In this study, we utilized our autochthonous mouse tumor model using in utero electroporation (IUE) of the embryonic mouse brain to explore these questions. Using rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) targeting HA-tagged ZFTA-RELA fusion in our IUE model, we demonstrate that both canonical and non-canonical NFkB proteins interact with ZFTA-RELA protein in ZFTA-RELA fusion ependymoma. Focusing on select key NFkB proteins, we performed chromatin immunoprecipitation sequencing (ChIP-Seq) targeting p50/NFkB1, a protein that partners with RELA/p65 in the canonical NFkB pathway, revealing that p50/NFkB1 regulatory programs define active genes that are both distinct from and shared with the ZFTA-RELA fusion protein. Functionally, we performed CRISPR-CAS9 knock out (KO) of p50/NFkB1 and identified no phenotypic effect, as KO lines demonstrated no growth impairment. Furthermore, NFkB targeting drugs did not impair tumor growth. Given these findings, suggesting redundant transcriptional programing, we identified that ZFTA and RELA intersect with TEAD transcription factor programs to activate YAP signaling and that p50 localizes to YAP-TEAD pathway members. Targeting TEAD 1 and 4 with ChIP-Seq, we found that TEAD 1 and 4 co-regulate p50/NFkB1 and ZFTA-RELA target genes. Finally, we demonstrate YAP pathway activation across all supratentorial ependymoma, including ZFTA-RELA ependymoma. Our pathway analysis consistently converged on YAP/TEAD pathways, suggesting collaboration of ZFTA-RELA fusion with YAP/TEAD in transcriptional regulation for these tumors. Targeting YAP/TEAD may therefore represent a promising therapeutic strategy for ZFTA-RELA fusion ependymoma.
LGG-08. TARGETED THERAPY IN BRAFV600E-DRIVEN PEDIATRIC GLIOMAS: UNCOVERING MECHANISMS OF RESISTANCE THROUGH A MULTI-OMIC APPROACH
Authors: Monica Capogiri, Andrea De Micheli, Ernesto Berenjeno-Correa, Andreas Postlmayr, Ana Sofia Guerreiro Stücklin
Journal: Neuro-Oncology (2023)

Abstract BRAFV600E is a key oncogenic mutation, detected in both pediatric low-grade gliomas and high-grade gliomas. Targeting the Ras-BRAF-MAPK pathway with BRAFV600E-specific inhibitors, such as Dabrafenib, is a therapeutic strategy increasingly used in clinical practice. However, therapy failure often emerges in patients, and the mechanisms driving drug resistance remain elusive. We apply a multi-omic approach to understand the evolution of BRAFV600E glioma cell lines and ex-vivo patient-derived cultures under BRAF inhibition. To recapitulate the clinical situation and decipher mechanisms of acquired resistance, we chronically expose BRAFV600E-positive glioma cells to a sublethal dose of Dabrafenib (IC20) and generate drug-resistant cell lines. We then profile the kinome (Pamgene microarray) and the transcriptome (bulk RNAseq) of resistant versus wildtype cells: in addition to reactivation of the Ras-BRAF-MAPK pathway, we observe increased activation and expression of PDGFRB and Src family kinases (SFK) in the Dabrafenib-resistant phenotype. To identify and track the longitudinal evolution of drug-resistant states, we further assess the evolution of glioma cell subpopulations under therapeutic pressure and profile consecutively collected samples (day 0; day 2; day 10; day 30 of treatment; and 10 days post-treatment) using single-cell transcriptomics (10x Chromium system, 10x Genomics). By profiling BRAFV600E glioma cells pre-, on- and post-treatment, we find that therapeutic pressure induces changes in cell subpopulations from early stages, and these changes are selected over time. Consistent with our kinome and bulk RNAseq findings, we confirm the role of PDGFRB in driving Dabrafenib resistance in a subset of cells. Furthermore, when off-treatment, the cells recapitulate the untreated status, indicating that resistance is a temporary, drug-dependent, phenomenon relying on the kinome rewiring. By dissecting the pro-survival role of the PDGFR/SFK axis upon Dabrafenib treatment, we will provide valuable mechanistic and therapeutic insights into targeted therapies for children with BRAFV600E gliomas.
IMMU-23. RESEARCH ON MULTI-ANTIGEN T CELL INFUSION AGAINST NEURO-ONCOLOGIC DISEASE (ReMIND)
Authors: Conrad Russell Cruz, Stephanie Gomez, Ashley Geiger, Melanie Grant, Rachel DiCioccio, Maria Fortiz, Haili Lang, Anushree Datar, Abeer Shibli, Emily Reynolds, Christopher Lazarski, Mariah Wachspress, Gloria Pezzella, Daisy Gomez, Jay Tanna, Fahmida Hoq, Patrick Hanley, Lindsay Kilburn, Brian Rood, Roger Packer, Catherine Bollard, Eugene Hwang
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION Pediatric patients with recurrent or progressive central nervous system (CNS) tumors have poor prognoses and clearly require improved therapies. Previous studies that used ex vivo expanded T cells show promising efficacy against viral infections. The polyclonal nature of these T cells, capable of recognizing multiple antigens, can be of potential benefit to patients with high-risk brain tumors, where intratumoral heterogeneity plays a prominent role in therapeutic resistance. METHODS Patients with CNS malignancies received T cells in a phase I dose escalation study (NCT03652545). The safety and feasibility of infusing ex vivo expanded, autologous T cells was determined in patients with newly diagnosed diffuse intrinsic pontine gliomas (DIPGs, Arm A, infused up to 5 months post irradiation) or recurrent/progressive non-brainstem CNS malignancies with (Arm C) or without (Arm B) lymphodepletion. RESULTS As of April 2023, 46 patients were enrolled on study. A total of 30 patients received infusions (8 in Arm A, 18 in Arm B, 4 in Arm C) that were well tolerated. One patient experienced a severe potentially-related adverse event (tumor swelling). In Arm A (DIPG), median OS was 12 months post-diagnosis (one patient survived for 31 months). In arm B, median OS was 11 months post T cell infusion, with 6 patients still alive (longest four years after treatment). In Arm C, 3/4 patients remain alive 4+ months from infusion (one patient had a potential pseudoprogression based on scans). CONCLUSIONS Autologous T cells can be expanded from pediatric patients with CNS malignancies and are well tolerated. Data suggests that TAA-T products may induce an anti-tumor response, with or without lymphodepletion, and prolong survival. Efforts are ongoing to analyze immune correlates which are focused on evaluating circulating T cell clones and investigating changes in peripheral blood gene signatures and circulating plasma proteins.
DIPG-30. HIF2 OVEREXPRESSION DICTATES AGGRESSIVENESS ADDITIONALLY TO TP53 MUTATIONS IN H3.3K27M PEDIATRIC HIGH-GRADE GLIOMAS THROUGH RAS-MAPK AND WNT/BCATENIN PATHWAYS
Authors: Quentin Fuchs, Stephanie Legras, Benoit Lhermitte, Romain Vauchelles, Erika Cosset, Lucas Gorka, Hassiba Outilaft, Izzie Jacques Namer, Eric Guerin, Carole Mura, Hélène Burckel, Georges Noel, Youssef Hibaoui, Anis Feki, Agathe Chammas, Thibaut Wolf, Andres Hugo Coca, Sophie Foppolo, Monique Dontenwill, Natacha Entz-Werlé
Journal: Neuro-Oncology (2023)

Abstract Diffuse midline (DMG) and brainstem (DIPG) high-grade gliomas (HGG) bearing H3.3K27M driver mutation are aggressive and uncurable brain tumors. We evidenced by the past HIF-2a and its transcriptional gene, EPAS1, as a marker of resistance when targeting mTor/HIF-1a pathway. To understand HIF-2α potential role in chronically active hypoxic environment in DIPG/DMG, we investigate its status in a cohort of pediatric HGGs comprising notably H3.3K27M mutant tumors and in their paired in vitro derived models. Using concomitantly the low-input chromatin immunoprecipitation sequencing method CUT&amp;RUN, RNAsequencing and metabolomics, we profiled the landscape of promoters and pathways regulated by HIF-2a in HGGs, where H3.3K27M and TP53 mutations are associated. Elucidation of HIF-2a downstream genes reveal statistically significant pathways linked to DIPGs (e.g., mTor and canonical Wnt pathways) and to DMGs (glutamatergic synapse and non-canoncial Wnt signaling). Finally, HIF-2a was evidenced as a new therapeutic target opening the path for its use concomitantly to irradiation.
DIPG-32. PRECLINICAL TESTING OF THE EFFICACY AND SAFETY OF CRISPR/CAS9 GENE EDITED CAR-T CELL THERAPY FOR DIFFUSE MIDLINE GLIOMA (DMG)
Authors: Ilango Balakrishnan, Lillie Leach, Angela Pierce, Senthilnath Lakshmanachetty, Krishna Madhavan, Susan Fosmire, Hannah Chatwin, Adam Green, Terry Fry, Rajeev Vibhakar, Eric M Kohler, Sujatha Venkataraman
Journal: Neuro-Oncology (2023)

Abstract DMGs are highly aggressive and difficult-to-treat brain tumors in children. Recent advances in Chimeric Antigen Receptor (CAR) expressing T cell therapy suggest application for brain tumors. Recent studies also demonstrate feasibility of GD2, Her2 and B7H3 CAR-T infusions in childhood brain tumors. We identified and developed a novel CAR-T therapy, targeting the CD99 antigen, which is homogenously expressed at high levels on DMG tumor cells. These CAR-T cells showed initial clearance of tumor, but the long-term persistence and anti-tumor efficacy of these CAR-T cells in DIPG xenografts were limited due to fratricide, as T cells also express CD99. To overcome this obstacle, we have further optimized a protocol in which we first knock-out CD99 from the human donor T cells using CRISPR-cas9 gene-editing and subsequently transducing with our CD99 virus in the pure population of CD99KO T cells. Systemic delivery of these gene-edited CAR-T cells showed enhanced in vivo persistence with complete clearance of tumor in DMG mouse models, and no tumor recurrence was seen well-beyond the time frame of expected tumor recurrence after treatment with un-edited CD99 CAR-T cells. In addition, loco-regional delivery of these gene-edited CD99 CAR-T cells when administered directly to the 4th ventricle, even at a low dose, showed similar anti-tumor efficacy with significantly increased animal survival. These data suggest a regional approach analogous to Omaya reservoir administered drug in humans may be a promising alternative approach to limit any toxicity.
RARE-08. MULTI-INSTITUTIONAL ANALYSIS OF PEDIATRIC RELAPSED/REFRACTORY CENTRAL NERVOUS SYSTEM GERMINOMA
Authors: Mary Claire McGlynn, Mohammad H Abu-Arja, Sumanth Nagabushan, Mohamed Saad Zaghloul, Ahmed Elhemaly, Kelsey Bertrand, Amar Gajjar, Hamidah Alias, Andrea Cappellano, Richard Graham, Sofia Jares Baglivo, Vivek Bhadri, Dinisha Govender, Mohamed S Abdelbaki
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND Relapsed central nervous system (CNS) germinomas are rare with no universal agreement regarding management. We explore prognostic factors that may impact the treatment of patients with relapsed CNS germinoma. METHODS An international multi-institutional retrospective study of relapsed/progressive CNS germinomas was conducted. Data was summarized using descriptive statistics. Overall survival (OS) was evaluated using Kaplan-Meier and Fischer’s exact test to estimate odds ratios (OR) and 95% confidence intervals (CI). RESULTS Analysis included 21 patients (Male 71.4%) with relapsed/progressive germinomas from 7 sites. Median age at diagnosis was 15 years (interquartile range (IQR): 9.9-19) with 5% presenting with metastatic disease. Twelve patients (57.1%) achieved complete remission (CR) after initial therapy. Nineteen children (90.5%) suffered relapse. One (4.8%) suffered progression. The median time from diagnosis to relapse/progression was 21 months (range: 10-56 months) with 90.5% occurring within 24 months. 19 (90.5%) underwent chemotherapy, 9 (42.9%) bone marrow ablative therapy (HDCx), and 13 (61.9%) radiotherapy. At last follow-up, 88.9% of HDCx and 92.3% of radiotherapy recipients were alive. Of patients receiving radiation, 45% received whole ventricular irradiation, 25% craniospinal irradiation, and 5% focal irradiation (remainder unreported). Eleven children (52.4%) achieved CR after relapse/progression therapy and 16 (76.2%) were alive at last follow-up. Median time to last follow-up was 39 months (IQR: 18.43–89.50). Re-irradiation at relapse (OR=16, 95% CI: 1.27-200.9) and achieving complete response (CR) at relapse/progression (OR=4, 95% CI: 1.04-1.78) were associated with improved OS. CR after initial therapy (OR=0.857, 95%CI: 0.11-6.62) and HDCx at relapse/progression (OR=4, 95%CI: 0.36-44.13) were not associated with improved OS. CONCLUSIONS Relapsed CNS germinomas are radiosensitive and salvageable by re-irradiation at relapse. This ongoing multi-institutional study will contribute to existing knowledge about relapsed/progressive CNS germinomas and inform prospective clinical trials to improve outcomes for children with relapsed/progressive disease.
BIOL-11. PRECLINICAL MODELLING OF PEDIATRIC BRAIN TUMORS USING ORGANOID TECHNOLOGY
Authors: Mieke Roosen, Chris Meulenbroeks, Phylicia Stathi, Joris Maas, Julie Morscio, Jens Bunt, Marcel Kool
Journal: Neuro-Oncology (2023)

Abstract Molecular characterization has resulted in improved classification of pediatric brain tumors, leading to many novel (sub)types with distinct oncodriving events. To study tumor biology and to perform translational research on each of these tumors, preclinical models are essential. However, we are currently lacking sufficient models, especially in vitro, to represent each (sub)type and their heterogeneity. To generate large series of preclinical in vitro models for pediatric brain tumors, we are using organoid technology. Cells from patient samples and patient-derived xenograft samples have been taken into culture to establish 3D organoids using tumor type specific culture conditions. These organoid lines retain the molecular characteristics of the original tumor tissue. They can be used to perform high-throughput drug screens, genetic manipulations, and co-cultures with, for instance, immune cells. Viable tissue is not always available for all tumor (sub)types and specific oncodrivers. To circumvent this lack of tissue, we can also induce tumors in vitro. Therefore, we generate cerebral and cerebellar brain organoids from human pluripotent stem cells. These organoids mimic human developing brain cells and can be genetically manipulated to model different brain tumor types. These genetically engineered brain tumor models allow us to study the cellular origins of pediatric brain tumors and the different tumor driving mechanisms. Tumors induced in the brain organoids histologically and molecularly resemble human patient samples based on (single cell) transcriptomic analyses. Moreover, the tumor cells are able to establish xenografts in mouse brains. In summary, organoid technology provides a novel avenue to establish in vitro models for pediatric brain tumors. At the meeting we will present data for various new ependymoma, medulloblastoma and embryonal brain tumor organoid models.